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Early one morning in April, the former CIA agent sat inside a room at a seedy Ramada Inn in Norfolk, Virginia, smoking crack with a Glock 9mm service pistol in his shorts. He was 42 years old, three weeks into an epic bender, and believed he had only two choices in life: die or go to jail. With him was a young couple he'd met a few weeks earlier who only knew him as Dave – a guy with a raging two-ounce-a-week crack-and-cocaine habit and some serious boundary issues. "He would say, like, a lot of creepy things to me," the woman, Jessica, would later tell a local TV news reporter. "Like, when my boyfriend wasn't around, like inappropriate things." She also didn't know that she was about to witness the final act in the collapse of a man who had done and seen acts committed in the shadows of the War on Terror.

Andrew Warren was a rarity in the CIA's Clandestine Service – African-American, fluent in Arabic and relatively young for an agent who'd already spent nearly a decade chasing terrorists in Afghanistan, Egypt, Iraq and Algeria, so deep undercover that few of his friends or family knew the nature of his work. Throughout the wildest days of the fight against Al Qaeda, when the CIA ran torture, rendition and assassination programs from black sites around the globe, Warren was a key player, "the black Steven Seagal," in the words of one of his mentors.

But all that had ended 18 months earlier, in October 2008, when Warren was called back to America, charged with sexual assault – the government claimed he'd drugged and raped an Algerian woman while serving there as station chief – and fired from the agency.

Since then, another warrant had been issued, for indecent exposure: Warren had allegedly visited a Norfolk neighbor's house with his "genitals hanging out of his pants," the neighbor told the local news. He skipped a court date without telling his lawyers. His father had filed a missing-persons report.

Inside the hotel room, the phone rang. Jessica picked it up.

We are law-enforcement officers with the United States government, and we're here to arrest Andrew Warren. The rest of you, come out with your hands up.

Jessica and her boyfriend walked out into the sunlit parking lot "without incident," according to a court document, where a small army had gathered. There were agents from the U.S. Marshals Service, Diplomatic Security Service and the Bureau of Alcohol, Tobacco and Firearms. Snipers had positioned themselves out of sight, and a SWAT team in full-body armor was prepared to storm the room. As Warren stumbled out behind Jessica, a deputy U.S. marshal yelled commands.

Warren refused and, as the officers approached, ran, with six agents in pursuit. The marshal tackled him to the ground, and five other agents piled on. Warren lifted his shirt, revealing the Glock. He was tasered, cuffed, thrown in the backseat of a police sedan and delivered to a local hospital.

In June 2010, he was sentenced to 65 months in prison at Federal Correctional Institution Ashland in northeastern Kentucky. For the past two years, he's been desperately trying to get out of jail, arguing that he's innocent and feeling abandoned by the government that had trained him to play a dirty game.

Last August, Rolling Stone began a long e-mail correspondence with Warren. The story he tells, and that all available evidence confirms, presents a harrowing account of the morality-scrambling life of a covert operative in the age of enhanced interrogation and "black sites." Vice President Dick Cheney had famously ordered the agency to use "any means at our disposal" after September 11th, and Warren enthusiastically obliged. But in the end, a spy who'd been everywhere and seen everything wasn't brought down by the extralegal activities of the CIA – the drones, the kidnappings, the torture. He was undone by a sex crime.

Andrew Marvin Warren was born in the military town of Chesapeake, Virginia, in 1967. His ex-Navy father worked for the postal service. In ninth grade, Warren began attending a school with a majority white student body. He remembered "being bored" at Great Bridge High School, but he was popular, played in the school band and on the football and tennis teams, and studied tae kwon do.

Warren enrolled at Old Dominion University in 1986, where he found himself even more bored by academics. He began to party, eating mushrooms and drinking, and his grades tanked. He dropped out and, for three years, worked for a contracting business his father had started, before deciding to go back to school, at Norfolk State University in 1990. It was there that his path to the CIA really began. He became a history major and quickly emerged as one of the department's stars. "He was very impressive, interesting, hard-working and very careful," says Paul Clark, a retired military-officer-turned-professor who also noted Warren's ability to move smoothly between the black and white student communities. "He lived in both worlds." Warren was popular, especially with women, say friends from college. "Andrew is a handsome fellow, has all the manners and gestures," says Bill Alexander, another one of his professors. 'Women were crazy about him. He had to turn them away."

In 1993, he graduated summa cum laude, with a 3.9 GPA. While still an undergrad, Warren had spent the summer of 1992 studying history and political science at Indiana University. After graduating, he enrolled in the Near Eastern Languages and Culture master's program there. Around that time, he came to the attention of one of the CIA's "spotters," a de facto on-campus agency recruiter. He was a prime candidate for the agency: ambitious, an effortless overachiever, highly intelligent and a risk taker – and his dark skin and skill with languages made him ideally suited for assignments in the Middle East, a region that was moving closer to the center of the agency's attention.

He took his first trip to the Middle East, for a four-week program in Egypt, in 1993. The next year, he received a fellowship to spend the following two summers at Yarmouk University in Jordan, where he continued his Arabic studies. In 1996, after receiving his master's, he got a job as a language analyst for the National Security Agency. Warren was then hired by the CIA, according to court documents. By 1997, he'd gone into training, and in 1999 Warren's appointment as a foreign service officer was published in the Congressional Record.

Warren joined the CIA during a time when it was way more Burn After Reading than Zero Dark Thirty – a borderline incompetent intelligence service on a serious losing streak. It had missed the nuclear tests by India and Pakistan in 1998 and were caught stealing economic secrets from allies. (In 1995, four CIA officers were accused of espionage by France.) In the Middle East, the agency was involved in a foiled attempt to assassinate Saddam Hussein. Somalia ended badly, Rwanda ended worse and the Balkans were a punch line ("Q: How do you know there was an open bar in the war room during the bombing of Belgrade? A: They ordered Serbian food and bombed the Chinese embassy!").

As the CIA tried to find itself, the threat of international terrorism emanating from the Middle East, Africa, North Africa and Central and Southeast Asia grew with each strike: the first World Trade Center attack in 1993, the bombings of U.S. embassies in Kenya and Tanzania in 1998, and the 2000 attack on the USS Cole.

Warren, with his experience in the Middle East and fluency in Arabic, was ideally positioned to fight these new threats. His first undercover job was as a clandestine officer in Kuwait in 1999, where he worked an office job during the day and hunted for sources. He rose through the CIA ranks quickly, becoming a GS-14, a civilian rank equivalent to a lieutenant colonel in the Army. His superiors seemed to like him, and he hadn't made any big mistakes. But quickly, the day-to-day grind of espionage frustrated him – he didn't like having to answer to State Department officials, could barely contain his contempt for the ambassador and diplomatic security officers, got bored with attending embassy cocktail parties and would later claim the stress and boredom of being in Kuwait "exhausted" him. In short, there wasn't any action. He felt like he was running errands for D.C. big shots who didn't know what to do with the answers to the questions they asked. The overseas work took a toll on his personal life, too. He'd gotten married to a fellow operations officer he met while in training, but the relationship didn't survive the stresses of the overseas assignments and lasted only two years.

Warren left the CIA in 2001. During his final months at the agency, he wrote and self-published a spy novel, People of the Veil. He described himself on the book jacket as a "foreign service officer for the U.S. State Department" who had "worked with the National Security Agency." He told family and friends that he was leaving because he was worn out and wanted to make money. On August 1st, 2001, Warren took a job at Citigroup in New York, working out of its office on Wall Street. (Others weren't so sure he had ever left the CIA and believed he was just building up a deeper cover.)

A month later, on September 11th, 2001, Warren went to work and saw the Twin Towers fall. "I was five blocks away from the World Trade Center when the attacks happened," he wrote on his book's website. "When I saw the second plane hit, I knew it couldn't be an accident and had to be an act of terrorism. I didn't know if it was the first part of larger attacks. . . . …There were reports that car bombs were going off in the Battery Park area."

Before the day was out, Warren had received a call from the CIA's counterterrorism center, whose office in the World Trade Center had been lost in the attacks. The agency set up temporary headquarters on the USS Intrepid – the decommissioned aircraft-carrier-turned-museum docked in the Hudson River – and changed the focus of its activities from recruiting U.N. diplomats to tracking down potential terrorists in the tri-state area. Warren, fired up in the wake of the 9/11 attacks, eagerly arrived the next day to get his assignment. He was back in the agency, a spy again.

By the third week of September, the agency began inserting the first CIA teams into Afghanistan. But Warren was stationed in New York, where he worked with the Joint Terrorism Task Force – which teamed CIA agents with the NYPD to monitor "Muslims at places they eat, shop and worship," as the AP would later put it. (One NYPD agent infiltrated a white-water-rafting trip that was organized by Muslim students at New York's City College; other informants reported back to the NYPD-CIA operation from the campuses of Yale, Rutgers and the University of Pennsylvania, among others.)

Though he was glad to be back in the game, his contempt for the CIA hadn't subsided. During one stakeout, Warren expressed doubts about the ability of his bosses to prevent another terrorist attack. An FBI-agent colleague recalls Warren telling him the CIA "has some of the biggest weasels." "Drew was savage in his criticism of the CIA," the FBI agent says. "He told me flat out they were still fighting the Russians on 9/11." But overall, Warren was considered a major asset, and he made a good impression on his colleagues. Says the agent, "He was very well thought of by the guys."

In March 2002, Warren got called up to the big leagues. The Global War on Terror had started – and when CIA Counter-terrorism Center Chief Cofer Black said, "The gloves come off," and Vice President Cheney said that we'd play on "the dark side," they were speaking to guys like Warren. He left New York bound for the hottest spot in the world: eastern Afghanistan, near the Pakistan border. For an ambitious field agent, Afghanistan was the place to be: Kabul and Kandahar, the two biggest cities, had fallen, the Taliban was in disarray and the commanders thought they were closing in on bin Laden. In his 2006 book Jawbreaker, Gary Berntsen, who supervised the CIA team in Afghanistan, described leading Warren's wave of officers into the country. "On the day before departure, Cofer Black called me into his office and shut the door," he recalls. "He said, 'It's now your time to make war…. I want you killing the enemy immediately. I know how aggressive you are in everything you do. That's why I approved you to lead this team.'" Black told Berntsen to expect that a third of his team would be killed or maimed. Black's message was clear: Be as brutal as needed. "The modern battlefield is a terrible place," he said. "Bad things happen, and our Afghan allies are less than fully reliable. Am I clear?"

Warren's job was to make those bad things happen. Before he was sent to Afghanistan, he spent time at the CIA's training facility near Williamsburg, Virginia, to receive the paramilitary training CIA agents needed for their agency's new mission. "Those selected for deployment were sent for a week of training in map-reading, communications training and weapons training, focusing on Soviet-made arms," according to Berntsen.

Warren's team ran all over Afghanistan before they wound up in Gardez, a hard-scrabble Taliban town strategically located in a valley near the Pakistan border in one of the most dangerous parts of Afghanistan – the provinces of Paktika, Paktiya and Kunar. Warren was there as a sort of hybrid soldier-spy, collecting intelligence and meeting and recruiting tribal leaders and anyone else who could help in the hunt for bin Laden and Al Qaeda. In addition to going through stacks of documents, hard drives and pocket litter, they needed to interrogate prisoners and arm and train local mercenary forces to hunt bin Laden.

The operations Warren was involved in were only partially successful: bin Laden's trail had gone cold, but the relationships formed between the men from the CIA and the military, and the hard lessons learned, shaped the fast, brutally effective counterterror programs we've employed since. "Although he was not a trained soldier, he was required to act in that capacity, along with his job as an intelligence officer," according to the court-ordered psychiatric assessment of Warren, obtained by Rolling Stone. "He recalled that on the first day in [redacted] . . .… a grenade went off, blowing off the arm of one soldier and killing another."

Despite failing to get bin Laden, the U.S. government and media portrayed the early Afghanistan war as a great victory. The U.S. military began a series of operations around the country, including Operation Anaconda, designed to trap and destroy the remaining Al Qaeda fighters in Afghanistan. There was a darker, more secret side to those early days, too – the beginning of the enhanced interrogation program. After overthrowing the Taliban in 2001, there were hundreds of prisoners, and the CIA needed somewhere to hold them; and one of the biggest secret prisons would become the Gardez Detention Facility, where Warren lived for two months in 2002. Many of these detainees were hapless young men in the wrong place at the wrong time, or picked up on a tip or a hunch or for the bounty Americans gave. Some were not: What they knew could possibly lead to bin Laden. Often, however, the results were disturbingly wrong: Khalid el-Masri, a German citizen with Lebanese heritage, wound up in Afghanistan's notorious "Salt Pit" prison for five hellish months before being exonerated. (Warren declined to say if he was involved in the case of el-Masri.)

While he was there, Warren participated in what he would later describe as "severe interrogation techniques," or what human rights groups call torture. He moved among the different theaters of the hidden conflict, possibly including the secret prisons in friendly nations like Poland, Romania, Egypt, Algeria, Pakistan and Thailand. "The Paks said to us, 'We're going to put some dry ice on this guy. Want to watch?'" one U.S. official recalls. "We'd say, 'No way, we can't see this, we'll be in the other room.'"

All manner of tactics were tried at the Gardez Detention Facility. The tactics included kicks, punches, whipping with extension cords, forcing prisoners into stress positions, electric shock, prying off toenails, being rolled in snow. Warren later claimed his time in Gardez contributed to his "post-traumatic stress."

Warren had been shot at, seen men blown up and committed acts of brutality. But he survived, and even thrived, in Afghanistan. His evaluation for the period ending in June 2002 noted that he had "transformed himself into one of [the Directorate of Operations'] most knowledgeable [officers] on Islam, the Islamic militant target and counterterrorism." But the war in Afghanistan was quickly overshadowed by the Bush administration's next move: invading Iraq. Warren was sent in advance of the March 2003 invasion. Based in northern Iraq, Warren was assigned to one of the two CIA teams tasked with paving the way. Warren's job wasn't easy. Working with Kurdish militias, he identified bombing targets and tracked down Al Qaeda training camps. It was old-school OSS shit, blowing up rail stations, sabotaging equipment, liaising with opposition leaders on the ground. "It was a relatively intimate setting, small team, and I was base chief and busy as hell – basically I saw him on many occasions, interacted with him, joked with him, ate meals with him," recalled Charles Faddis, a CIA officer who worked with Warren in Iraq. "The only qualification: He was always a guy who seemed up, pumped, good sense of humor, hard-charging, wasn't an ass kisser, never attracted my negative attention."

In June 2003, Warren returned to New York for another stint with the terrorism task force. Ken Beeth, a 21-year CIA officer, was impressed: "Andrew had abundant qualities: formidable intelligence and work ethic, confidence, tireless dedication to the mission, a willingness to break china when necessary." These qualities worked wonders in a war zone but were less suited to navigating office politics back home. "An officer like this also creates antagonisms, and Andrew was still too junior to take the institutional and procedural risks he did," Beeth wrote in a letter to the court after Warren's arrest, requesting leniency on his behalf. (What Beeth means specifically is unclear. The rest of the paragraph is redacted.) Another factor a few of his friends and colleagues point to is the turbulence Warren may have endured in the largely white CIA leadership due to his race. One former CIA officer, when asked about Warren's "hall file" – Langley slang for water-cooler gossip – was blunt about a root cause of the antagonism. "He's African-American. I can't think of another at that [senior] level."

At the same time, his own personal universe was beginning to show signs of cracking. In New York, his home between overseas assignments, he shared an apartment with his sister Renee, a journalist and publicist. They were close: She helped Warren throw a party for his book, and her boutique PR firm was listed on Warren's author website. But his time overseas had changed him, and Warren's entire family noticed the difference. "He could never sleep. He told me that he had nightmares," his sister wrote in a letter to the court, describing how at night she could hear him screaming in Arabic through the paper-thin walls of the apartment. "He no longer felt safe in NYC – he was always watching his back." Warren advised Renee to change her routes back home because "the bad guys" were following him and, by extension, her. The paranoia was running deep – but his family didn't know if it was legit fear (Al Qaeda, after all, did have CIA agents on its hit list) or the beginning of a delusional fantasy.

Warren's older brother Lewis, a successful Wall Street executive, would later accuse the CIA of failing to take proper care of his brother. Lewis' letter to the court said, "He had recurring nightmares … of colleagues being blown up, violently, by machine-gun fire and high explosives – the fact that his company offered Andrew zero medical care is a disgrace."

The fact is, psychiatric help is not widely available to CIA agents – and as in the military, there is a stigma attached to admitting post-traumatic stress. Warren, his psychiatrist would later testify, dealt with his demons himself. "He was clearly self-medicating his symptoms of posttraumatic stress with alcohol," the doctor said. After his return to New York, Warren "began drinking more heavily and began questioning his prior use of severe interrogation techniques." (A CIA spokeswoman responds that the agency provides ample counseling services for its officers: "The idea now that the agency is in any way responsible for Mr. Warren's despicable actions – for which he was fired and pled guilty in a court of law – is preposterous.")

Despite his private unraveling, in 2004, Warren got his biggest promotion yet: second in command of the CIA's Cairo bureau. Even though he was operating undercover as a State Department official, this was no desk job: During his time there, according to court documents, he was involved in "periodic gun battles" on the streets of Cairo.

With his State Department cover, he moved in diplomatic circles, attending social events and hosting parties – in other words, old-school spying. But Cairo was not a great place for someone with PTSD. "He traveled in armored vehicles every day, which caused him to feel extremely claustrophobic. … He continued to have difficulty sleeping, as well as frequent nightmares, and acknowledged drinking and using Valium and Xanax that were readily available without a prescription for more severe anxiety," according to his psych report.

Seemingly unconcerned to his mental decline, the agency was grooming him to run a CIA station of his own, overseeing American agents and cultivating a network of local sources. After three years in Egypt, he was tapped to be the next station chief of Algiers, capital of another North African nation, Algeria.

In September 2007, Warren moved to a mansionlike home in Algiers provided by the U.S. diplomatic mission. Officially, he was just another senior embassy official; unofficially, as CIA station chief, he was the second-most-powerful American in the country. The operation was his to run, with little interference from the bureaucrats he'd come to despise. Algeria was a key ally – its authoritarian leader, President Abdelaziz Boute-flika, was an enthusiastic supporter of the War on Terror. The Algerians had spent a decade fighting Islamic radicals and were a natural partner the CIA could use to keep tabs on Al Qaeda: Islamic militants operated there, and drugs, weapons, girls, boys, diamonds and bootleg oil were all available on Algeria's black market.

Warren lived it up. He threw a party at his house that same month. One of the guests was a young Algerian woman with German citizenship. According to a statement the woman gave to Diplomatic Security Service investigators, Warren offered her several Jack and Cokes, which she drank.

After her last cocktail, she suddenly got sick, clamped her hand over her mouth and ran to the bathroom, puking in the toilet. Another woman followed her to the bathroom to help. Warren offered to let her stay the night in the guest room.

That was the last thing she remembered. Later, according to her statement, she woke up naked in bed, wondering what had happened. She had a headache and her vagina was sore. A used condom was in the garbage can beside the bed. She called her friend, who was staying in another spare bedroom, and showed her the used condom before getting dressed and leaving the house. She never saw or contacted Warren again, nor did she report what happened, according to the statement she submitted to investigators. She would later be referred to in court documents as Victim 1.

Five months later, another Algerian woman he had befriended in Cairo came to Algiers to pick up her parents and take them to Europe for a medical appointment. According to her statement, on February 17th, 2008, she stopped by Warren's house. He gave her a tour, then they sat on the couch to talk. Warren asked if he could take her photo. He snapped a photo with his phone, then offered her a drink. He walked to the kitchen, out of sight, and came back with two apple martinis. As they talked and drank, Warren offered her another drink. This time, she followed him to the kitchen. He quickly handed her a platter with crackers and asked her to take them to the living room.

While drinking the second martini, she felt faint. She needed to puke. She "began to pass in and out of consciousness." The next thing she remembered was finding herself on the floor in the upstairs bathroom. She couldn't move, but she could see and hear. Warren was standing over her, taking off her pants. She managed to say one word: "Leave," she told him.

'You'll feel better after a bath," Warren replied, taking off her boots, jeans and blazer. Her next memory was being out of the tub and struggling to put on her jeans. She blacked out again and woke up in Warren's bed. "Stop," she said.

"Nobody stays in my expensive sheets with clothes on," Warren replied, again taking off her jeans and underwear.

She kept asking Warren, "What's happening to me?"

After blacking out again, she found herself naked in the bed. According to the affidavit, Warren was "nude, on his knees," with an erection. "Use a condom," she said.

She woke up sometime later in Warren's bed "but did not understand what had happened." She got her clothes back on and drove home but doesn't remember how. According to her statement, on February 19th, 2008, she sent Warren a text message "accusing him of abusing her."

Warren sent one back: "I am sorry."

For the next seven months, Warren continued his job at the embassy. Then, on September 15th, 2008, Victim 2 visited the U.S. embassy in Algiers. She wanted to file a complaint: She claimed Andrew Warren had raped her. The news of the complaint circulated around the compound, making its way to a Marine who worked in the security office. After hearing about the complaint, the unidentified Marine told embassy officials that he'd heard a similar story about Warren from another woman: Victim 1 – who was then asked to file a complaint as well.

Without being told why, Warren was summoned back to Langley. His supervisor sat him down alone in a room and told him that he was being accused of rape. Warren insisted that both encounters were consensual. The CIA officer then escorted him to two diplomatic security-service agents who were waiting: Scott Banker and Danielle Pasquale. The agents demanded Warren give up his phone and laptop. Warren told Banker that he'd left his laptop in his hotel room but admitted it probably had photos of both women on it. After the interview, Warren gave his phone and laptop to Banker for forensic analysis.

The lab found "multiple photographs" of Victim 1 and Victim 2, "along with various other women," on his laptop and phone. Around the same time, the FBI was conducting a raid on his residence in Algiers. "During the search, agents recovered, among other items, apple-martini mix, multiple data-storage devices, including multiple computer hard drives, memory cards, Valium and Xanax and a handbook on the investigation of sexual assaults," according to the DSS investigation affidavit. The U.S. government claimed it also found child pornography, which Warren denied existed.

Warren argued that he was the victim of a "honey trap," a plot used by foreign governments to blackmail or entrap men by using attractive females. He also claimed that the Algerian intelligence chief had it in for him, feeling threatened by a black man who spoke Arabic and who was not as easily duped as the Americans the Algerians were used to dealing with. There is also a remote possibility that Warren may have believed that he was doing his job – recruiting sources, in these cases, through predatory sexual practices. When it came to Muslim women, after all, sex with a Western man, with photographic evidence, would provide serious leverage. The judge later noted Warren believed he could "get away with it" because he assumed the women would be too terrified to speak out.

As the investigation unfolded, Barack Obama was elected and a new director of the CIA, Leon Panetta, was appointed. Inside the State Department, U.S. officials panicked at what they saw as a potential international scandal: not just Andrew Warren's behavior, but the CIA's presence in Algeria. At the time, the U.S. military was launching AFRICOM, a new African command center – and the U.S. government was terrified it would be seen as an attempt to control African governments. State Department officials convened a meeting to spin the story. "Most of our local staff thought the story would pass relatively quickly, but the focus would shift from the reported incidents to questions of the CIA presence in Algeria," a cable made public by WikiLeaks stated.

In January 2009, news of the investigation was leaked to Brian Ross at ABC News. Warren was portrayed as a rapist and a criminal; Panetta, the new CIA director, was asked about the case at his confirmation hearing and said Warren should be fired. In March 2009, Warren was terminated. His psych report noted, "Following his being fired and charged with the current offense, he also became clinically depressed. When his depression and post-traumatic anxiety escalated and was not adequately controlled by alcohol alone, he turned to cocaine powder and then crack cocaine to escape from his severe anxiety and depression."

It's exceedingly rare for a CIA officer to be convicted of a crime other than espionage. In fact, there is currently only one other in prison. Warren's lawyers believed he would be able to cut a deal, perhaps beat the charge, saving him from prison and the government from having its darkest secrets spilled during a trial. 'We had a strong case," says Mort Taubman, one of Warren's many lawyers.

Warren, though, was convinced he was going to jail. Despondent, he slid right into the gutter, developing a stunning quarter-ounce-a-day crack habit. On April 3rd, 2010, just three weeks before his final arrest at the Ramada Inn, the Norfolk police were called after he allegedly exposed his penis to his neighbor. According to current documents, when the cops showed up, Warren gave an officer a fake Social Security number and an alias. He told the officer that he was an expert in martial arts, fluent in eight languages and had a disguise kit and a Glock pistol. He told the officer he worked for the CIA.

The officer thought Warren was insane. And in a way, he was right: The former agent was in the midst of a drug-fueled psychotic episode – but everything he said was true. "Crack got rid of the pain," he later told the judge. "As soon as I got sober, I did more. I was afraid I'd be arrested. I was afraid I'd be arrested, I'd have my bail revoked. I was going to jail anyway, so I just began using crack."

After his bust, on April 27th, 2010, he appeared in a wheelchair at the courthouse. The feds piled on the charges: resisting arrest, possession of a firearm, and drug paraphernalia. His lawyers cut a deal: He'd plead to one count of abusive sexual contact and one count of using cocaine while possessing a firearm and avoid a trial. More than 24 colleagues and friends wrote letters asking for leniency. The missive sent by his friend, hedge-fund manager Ed Williams, is typical: "I am not aware of all the details, but the media describes a person that I do not know or recognize. The Andrew that I know has led an exemplary life. A life of fighting for his country, a life of helping others, a life of giving back, a life of teaching others, a life worth saving. I know Andrew can rebuild his life if given the opportunity to prove himself again – he has a strong family and many friends to support him if given the opportunity."

Warren's defense argued that the stress of a life lived on the dark side – the interrogations, the renditions, seeing friends killed – derailed him. The prosecutor recommended a 33-month sentence, but the judge, Ellen Huvelle, slapped him with 65 months. "It is rare that the court is confronted by an individual who has accomplished so much and fallen from grace so far," she said. In Algeria, she said, "you had a house, you had diplomatic immunity, you were an important person in the community. I think you took a calculated risk that it would not be discovered and that she would not complain. Because of her religion, I think you are well aware of – you've been in Muslim countries – the extreme humiliation, pain and ostracism a person like this would suffer if the full facts ever became known." She concluded: "The public needs to be protected [from Andrew Warren]."

In March 2011, he arrived at Ashland's federal correctional institution in Kentucky for a five-year stay.

On Saturdays, inmates at the Federal Correctional Institution Ashland get a meatball sub for lunch, a major weekly treat for the approximately 12,000 prisoners locked up in the two-story brick low-security prison near the border of Ohio and West Virginia. Among the prison population, ironically, are both Warren and Rafiq Sabir, a doctor linked to Al Qaeda who is serving 25 years on terrorism charges. After spending time in solitary upon arrival, Warren now resides in Cell Block D, dressed in a tan jumpsuit like every other inmate.

In January, I went to Ashland to interview Warren. We had been e-mailing for almost six months, and I had explained to him that I didn't think his story had been fully told and that it sounded like he'd had a fascinating Zelig-like career, witnessing or participating in historical events, from enhanced interrogation and 9/11 to Iraq and Afghanistan. I wondered, "Could he have actually been set up?" Or was the simplest answer the most likely, that he was a sex criminal? His defenders, like an Algerian official who worked at the embassy, insisted "the Algerian chief did this to him." Dozens of his friends testified to his character and remain in complete disbelief that he could have committed the crimes he was accused of. At least I wanted to ask him these questions and how he felt about them.

To start the correspondence, I wrote Warren a letter, asking for permission to be added to his Bureau of Prisons e-mail contact list, through a system called Corr-Links. He gave me his approval, and we sent half a dozen e-mails to each other. I sent him copies of my books and articles; he mentioned that he reads Rolling Stone, including a recent piece on solitary confinement. He told me about the challenges he faced in solitary, of the "roaches and rats" he claims he saw while in the hole: "Solitary confinement…was not a good experience," he wrote. "It was not because of any punitive reason but because they did not know what to do with me because of my skill set…. I was locked down for 23 hours a day, which was a challenge for someone with PTSD."

Warren's e-mails generally displayed the intelligence his friends consistently mentioned. Then, like a good case officer working a source, he started to mirror my language, beginning his e-mails with the same salutations I used. "Dear Mr. Warren," I wrote him. "I hope this letter finds you well." "Dear Michael," he wrote back, "I hope this email finds you well." He referred circumspectly to months spent in Iraq before 2003 and "sensitive issues" he wasn't at liberty to discuss yet, apparently fearful of more CIA retribution and disclosing classified information. I got the strong sense he felt betrayed by the government.

In December, his sister confirmed he'd sit down for an interview at the beginning of the new year. He e-mailed me he'd been working on his own memoir: "I continue to write parts of my story – Kuwait, Afghanistan, working with the FBI/ NYPD in the Joint Terrorism Task Force, Iraq, Egypt, Algiers and a myriad of other places," he wrote. "My fall has been the greatest teaching experience of my life, and I want to give you the flavor of where I have traveled, both mentally and spiritually. I am not the same individual who was arrested on 26 April 2010."

In early January, I headed to Ashland as we had arranged. I was halfway there when he sent me a panicked e-mail, canceling the visit. Before all this, Warren told me he'd just lost an appeal – his secret hope had been to do the interview once he was out of prison. He also said that any publicity would put his life at risk. "I did not want to have a story written while I was still incarcerated because of the safety factor," he wrote me. "Being incarcerated with individuals who are convicted of terrorism crimes as well as some here who have no love of former government officials or those associated with the government would put me in a potentially volatile and dangerous situation."

I suggested we see each other in person to discuss the story. Me and my colleague Matt Farwell were allowed into the prison, escorted through three security doors and given a neon-yellow stamp on our hands. We were not allowed to bring anything but a pen and paper. Then we waited in the visiting room for Warren to come out. He didn't. I was surprised – he'd e-mailed me that he had reservations about discussing sensitive material in the visitors' room, but I had expected after months of e-mailing he'd at least meet me in person. I asked the guard how often prisoners refused visitors. "It's the second time I can remember it in over 20 years," the guard said. Later that day, a lawyer claiming to represent Warren and his family telephoned me. "Cease and desist," he told me. "You will not be getting a statement from Andrew Warren." The former CIA spy has 22 months left on his sentence.